1XIW

Crystal structure of human CD3-e/d dimer in complex with a UCHT1 single-chain antibody fragment

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

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This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of a human CD3-epsilon/delta dimer in complex with a UCHT1 single-chain antibody fragment.

Arnett, K.L., Harrison, S.C., Wiley, D.C.

(2004) Proc Natl Acad Sci U S A 101: 16268-16273

  • DOI: 10.1073/pnas.0407359101
  • Primary Citation of Related Structures:  
    1XIW

  • PubMed Abstract: 

    • The alpha/beta T cell receptor complex transmits signals from MHC/peptide antigens through a set of constitutively associated signaling molecules, including CD3-epsilon/gamma and CD3-epsilon/delta. We report the crystal structure at 1.9-A resolution of a complex between a human CD3-epsilon/delta ectodomain heterodimer and a single-chain fragment of the UCHT1 antibody ...

    The alpha/beta T cell receptor complex transmits signals from MHC/peptide antigens through a set of constitutively associated signaling molecules, including CD3-epsilon/gamma and CD3-epsilon/delta. We report the crystal structure at 1.9-A resolution of a complex between a human CD3-epsilon/delta ectodomain heterodimer and a single-chain fragment of the UCHT1 antibody. CD3-epsilon/delta and CD3-epsilon/gamma share a conserved interface between the Ig-fold ectodomains, with parallel packing of the two G strands. CD3-delta has a more electronegative surface and a more compact Ig fold than CD3-gamma; thus, the two CD3 heterodimers have distinctly different molecular surfaces. The UCHT1 antibody binds near an acidic region of CD3-epsilon opposite the dimer interface, occluding this region from direct interaction with the TCR. This immunodominant epitope may be a uniquely accessible surface in the TCR/CD3 complex, because there is overlap between the binding site of the UCHT1 and OKT3 antibodies. Determination of the CD3-epsilon/delta structure completes the set of TCR/CD3 globular ectodomains and contributes information about exposed CD3 surfaces.

    Organizational Affiliation: 

    Department of Biological Chemistry and Molecular Pharmacology, Howard Hughes Medical Institute, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA. arnett@crystal.harvard.edu



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 epsilon chainA, E105Homo sapiensMutation(s): 0 
Gene Names: CD3E, T3E
UniProt & NIH Common Fund Data Resources
Find proteins for P07766 (Homo sapiens)
Explore P07766 
Go to UniProtKB:  P07766
PHAROS:  P07766
GTEx:  ENSG00000198851 
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UniProt GroupP07766
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 delta chainB, F79Homo sapiensMutation(s): 0 
Gene Names: CD3D, T3D
UniProt & NIH Common Fund Data Resources
Find proteins for P04234 (Homo sapiens)
Explore P04234 
Go to UniProtKB:  P04234
PHAROS:  P04234
GTEx:  ENSG00000167286 
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UniProt GroupP04234
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
immunoglobulin light chain variable regionC, G108Mus musculusMutation(s): 0 
Gene Names: UCHT1
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
immunoglobulin heavy chain variable regionD, H122Mus musculusMutation(s): 0 
Gene Names: UCHT1
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.874α = 90
b = 79.326β = 90
c = 150.747γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation